Thanks, Jason. It works if I specify a host file. But there is another
issue: qstat -f showed that the job was running on other nodes. Actually
sander.MPI is running on the nodes I specified. Will this probably mess up
the PBS queue system?
Regards,
William
On Tue, Sep 13, 2011 at 5:38 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>
> Don't use nohup in a PBS script. Also, I would suggest passing mpirun the
> $PBS_NODEFILE as the hostfile/machinefile/whatever OpenMPI likes to call
> it. That will tell mpirun where to lock the threads (rather than just
> dumping them all on the same node).
>
> HTH,
> Jason
>
>
> >
> > Does anybody has ideas what went wrong?
> >
> > Thanks,
> > William
> > _______________________________________________
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> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Sep 14 2011 - 08:30:03 PDT
